The Sand Wand was my favorite, like everyone else (although I thought the Spirit Flute was the best instrument in the history of Zelda). The thing about it was that it's something we rarely see. It wasn't just a unique item, it was an environmental item. We never see those. Even items like the Magnetic Gloves can at best manipulate objects, not the environment itself. While you could only manipulate sand, it was still something different.
It led to more intriguing puzzles IMO, because more so than before the environment itself was essentially your playground, and if this concept is taken further in the future (and god I hope it is) I think it could make for some incredibly challenging and creative puzzles.